Volume 1, Issue 2, Pages 141-151 (August 2015) Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells  Li Ding, Maciej Paszkowski-Rogacz, Maria Winzi, Debojyoti Chakraborty, Mirko Theis, Sukhdeep Singh, Giovanni Ciotta, Ina Poser, Assen Roguev, Wai Kit Chu, Chunaram Choudhary, Matthias Mann, A. Francis Stewart, Nevan Krogan, Frank Buchholz  Cell Systems  Volume 1, Issue 2, Pages 141-151 (August 2015) DOI: 10.1016/j.cels.2015.08.002 Copyright © 2015 Elsevier Inc. Terms and Conditions

Cell Systems 2015 1, 141-151DOI: (10.1016/j.cels.2015.08.002) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 1 Genome-Scale RNAi Screen in Mouse EpiSCs (A) Illustration of important shared and divergent attributes in ESCs and EpiSCs. Genes for exemplified indicated classes and pathways are shown. The GSK-3 inhibitor (CHIR99021) and MEK inhibitor (PD0325901) that maintain self-renewal of ESCs are indicated. (B) Comparative analysis of the screen results in EpiSCs and in ESCs. The y axis represents the average Z scores for the GFP intensity for each targeted gene. Upregulated (Z score >2) or downregulated (Z score <−2) Oct4 expression is depicted in yellow and blue, respectively. Note the large number of knockdowns that upregulated Oct4 expression in the EpiSCs screen. Cell Systems 2015 1, 141-151DOI: (10.1016/j.cels.2015.08.002) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 2 Categorization of Validated Oct4 Modulators (A) Phenotypic comparison of ESCs and EpiSCs. Indicated categories classify the genes based on their changes of Oct4 expression in ESCs and EpiSCs. Knockdowns that upregulate Oct4 expression are shown in yellow. Knockdowns that downregulate Oct4 expression are shown in blue. The color intensity scales with the intensity of the phenotype. (B) Examples of knockdowns for different categories. Oct4 expression (green) after transfection with indicated esiRNAs in ESCs and EpiSCs is shown by immunostaining (upper) and quantified by FACS (lower). DAPI was used to stain cell nuclei (blue). Scale bars are 20 μm. Cell Systems 2015 1, 141-151DOI: (10.1016/j.cels.2015.08.002) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 3 Epistasis Map of Oct4 Modulators (A) E-MAP profile of Oct4 modulators in EpiSCs. GIs are illustrated as blue squares (negative GIs; synergistic), yellow squares (positive GIs; buffering), and black (neutral GIs). The numbers on the color bar indicate GI scale. Proteins known to form complexes are highlighted with a color code. (B) Validation of the positive GI between Apc and Ctnnb1 by quantitative western blot. Oct4 protein levels were quantified and normalized to Gapdh after treatment with indicated esiRNA combinations. The non-targeting LUC esiRNA was used as control. The numbers represent fold changes in respect to LUC transfected cells. (C) Validation of the negative GI between Brd4 and Trrap by quantitative western blot. Oct4 protein levels were quantified and normalized to Gapdh after treatment with indicated esiRNA combinations. The non-targeting LUC esiRNA was used as control. The numbers represent fold changes in respect to LUC transfected cells. Note the synergistic upregulation of Oct4 after co-depletion of Brd4 and Trrap. Cell Systems 2015 1, 141-151DOI: (10.1016/j.cels.2015.08.002) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 4 PLD of Oct4 Modulators (A) PLD matrix of Oct4 modulators. Protein-level changes are illustrated for each cell line/esiRNA combination with increases marked in yellow and decreases marked in blue. The color intensities scale with the intensity of the changed protein level. Proteins known to form complexes are highlighted with a color code. (B) PLD between Cnot2 and Cnot3. Depletion of Cnot3 leads to a decrease in Cnot2, whereas depletion of Cnot2 results in an increased in Cnot3 (upper). Quantification of indicated mRNA levels after Cnot2 knockdown are shown in the lower panel. Error bars represent SD from triplicates. Individual Z scores are shown in each square. (C) PLD between Ctr9 and Cpsf3. Depletion of Ctr9 leads to a decrease in Cpsf3 and vice versa (upper). Quantification of indicated mRNA levels after Ctr9 knockdown is shown in the lower panel. Error bars represent SD from triplicate samples. Individual Z scores are shown in each square. (D–G) FACS quantification of the expression of BAC-tagged EpiSCs (left) or ESCs (right) after transfection with indicated esiRNAs. The tagged gene is presented in the respective Fl1 channels. The peaks show results after Luc transfection (control; blue) and transfection with indicated esiRNAs (red). Cell Systems 2015 1, 141-151DOI: (10.1016/j.cels.2015.08.002) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 5 Multiparametric Integration of Omics Data (A) Graphical presentation of hierarchical cluster analysis of indicated Omics data. A binary distance metric was used for the localization data, and a Euclidean distance metric was employed for all other datasets. Components of known protein complexes are highlighted with the same color. (B) Tox4 depletion decreases Oct4-GFP expression in ESCs and EpiSCs. Results from quantitative FACS analyses using two independent esiRNAs (Tox4-1 and Tox4-2) and the luciferase control esiRNAs (LUC) in Oct4-Gip ESCs and OE7 EpiSCs are shown. Values are means ± SD from triplicate samples. ∗∗ indicates significance (p < 0.01) based on the Student’s t test. (C) Phenotypic analysis of Tox4 knockdown in ESCs and EpiSCs. The upper panel shows brightfield microscopic images of EpiSCs treated with indicated esiRNAs. Note the bigger and flatter cells, loss of cell-to-cell contact, and failure to form tight colonies in the Ctr9- and Tox4-transfected cells. Scale bars are 50 μm. The lower panel shows images of alkaline phosphatase stained ESCs after transfection with indicated esiRNAs. (D) Tox4 regulates the expression of developmental genes. Gene Ontology term analysis of differentially regulated pathways after Tox4 knockdown is shown. Fold enrichment of genes in each category and p values are presented. Cell Systems 2015 1, 141-151DOI: (10.1016/j.cels.2015.08.002) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 6 Tox4 Physically Interacts with the Paf1C (A and B) Reciprocal Co-IPs of GFP-tagged Ctr9 and Tox4 in EpiSCs (A) and in ESCs (B) are shown. The IP eluates and corresponding input were probed with antibodies against Tox4, Ctr9, and Gapdh. Gapdh served as a reference for Co-IP enrichments. GFP-tagged Tox4 is marked by ∗, and endogenous Tox4 is marked by X. (C and D) Proteomic profiles of Tox4 and Ctr9 interacting proteins. Results for indicated preys are presented as volcano plots showing (−log10 p value) versus (log2 protein enrichment [GFP/WT]). A hyperbolic curve (red lines, defined by threshold value = 0.01 and S0 = 2) separates specific prey-interacting proteins from background. Significant enrichments of Paf1C core components are presented in orange. Bait proteins are highlighted in bold. Cell Systems 2015 1, 141-151DOI: (10.1016/j.cels.2015.08.002) Copyright © 2015 Elsevier Inc. Terms and Conditions